User: 948077241

gravatar for 948077241
9480772410
Reputation:
0
Status:
New User
Last seen:
5 days, 4 hours ago
Joined:
3 months ago
Email:
9********@qq.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by 948077241

<prev • 16 results • page 1 of 2 • next >
0
votes
0
answers
40
views
0
answers
How to skip vep-annotating step for vcf2maf
... I have got my `variant.vcf` annotated at the web of `VEP` and downloaded the annotated `variant.annotated.vcf` file. My problem is : now I want to convert my `variant.annotated.vcf` to `maf` format. I used `vcf2maf` but it cannot skip the vep-annotating step even that I have a copy of `variant.anno ...
vcf2maf written 5 days ago by 9480772410
0
votes
1
answer
157
views
1
answers
Comment: C: How can I split WES FASTQ file into sub-files for each chromosome ?
... Thank you for your meticulous explanation! It's more understandable for me and helps a lot. And now I basically know how this loop work step by step. Thank you! ...
written 5 days ago by 9480772410
0
votes
1
answer
157
views
1
answers
Comment: A: How can I split WES FASTQ file into sub-files for each chromosome ?
... So...my question now is somewhat weird. Let's talk about it in more detail (may be profix, but I cannot figure out some better way) Given I have two raw data that are in fastq format. And my target is to split them (paired-end data) and get a sub-file containing data from chr10 only. So I firstly ...
written 5 days ago by 9480772410
0
votes
0
answers
113
views
0
answers
Comment: A: Error when split WES data into sub-files
... I have checked that my chr10.bam exactly has lots of reads from chr10. But I don't know how to check my chr10 reference. And I suppose that samtools faidx has produced an index file (.fai format) for chr10 reference? Before running BWA , I also follow this command: bwa index chr10.fasta As fo ...
written 6 days ago by 9480772410
0
votes
0
answers
113
views
0
answers
(Closed) Error when split WES data into sub-files
... I have got my WES data and now I want to split my data into a sub-file containing data only from chr10 (both my data that in fastq format and the reference ucsc.hg19.fasta ). My code was like this: for my data: I map it to ucsc.hg19.fasta by BWA bwa mem ~/reference/ucsc.hg19.fasta ~/input/ ...
fastq wes reference bwa bam written 6 days ago by 9480772410
0
votes
1
answer
157
views
1
answers
Comment: C: How can I split WES FASTQ file into sub-files for each chromosome ?
... OK! Thanks a lot! I'll go and search details about it. ...
written 7 days ago by 9480772410
0
votes
1
answer
157
views
1
answers
Comment: C: How can I split WES FASTQ file into sub-files for each chromosome ?
... Thank you! It works perfectly! But what if I want to split files from gatk bundle by chromosomes as well, taking ucsc.hg19.fasta and dbsnp_138.hg19.vcf for examples. What tools should I use? It seems samtools could not index such files in vcf format. ...
written 7 days ago by 9480772410
0
votes
1
answer
157
views
1
answers
Comment: C: How can I split WES FASTQ file into sub-files for each chromosome ?
... Thanks a lot! It helps a lot! And I am working on it now. BTW will samtools view region work the same if I need to split gatk bundles as well, like ucsc.hg.19 ? ...
written 7 days ago by 9480772410
0
votes
1
answer
157
views
1
answers
Comment: C: How can I split WES FASTQ file into sub-files for each chromosome ?
... But if I have align it to a reference by BWA, it will become one (.bam) file. Will it produce both reverse and forward (.fastq) files if I convert the aligned (.bam) file back to (.fastq) file? ...
written 7 days ago by 9480772410
3
votes
1
answer
157
views
1
answer
How can I split WES FASTQ file into sub-files for each chromosome ?
... I have get my WES data in fastq format. But now I need to split it into sub-files by chromosome, like chr1.fq , chr2.fq . Please give me some advice. I work on linux system, please specify what tool I need or even the comands recommended if it is convenient. Thanks a lot! ...
fastq wes split chromosome written 7 days ago by 9480772410

Latest awards to 948077241

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2213 users visited in the last hour